CI
61eb413b0a
Build pipeline: viash-hub.htrnaseq.v0.11-tl5df
Source commit: 213fd5f7d0
Source message: Merge remote-tracking branch 'origin/main' into v0.11
72 lines
1.9 KiB
YAML
72 lines
1.9 KiB
YAML
name: combine_star_logs
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namespace: "stats"
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authors:
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- __merge__: /src/base/authors/dries_schaumont.yaml
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roles: [ author, maintainer ]
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argument_groups:
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- name: "Arguments"
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arguments:
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- name: "--barcodes"
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type: string
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multiple: true
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required: true
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description: |
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Barcodes responding to the respective log files.
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- name: "--star_logs"
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type: file
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multiple: true
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required: true
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description: |
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Paths to the STAR log files (most frequently called Log.final.out)
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direction: input
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example: "Log.final.out"
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- name: "--gene_summary_logs"
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direction: input
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type: file
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multiple: true
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required: true
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description: |
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Paths to the Summary.csv files from the STAR Solo output. Can be found in
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the 'Solo.out/Gene' folder relative to the root of the STAR output directory.
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example: "Summary.txt"
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- name: "--reads_per_gene_logs"
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direction: input
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type: file
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multiple: true
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required: true
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description: |
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Paths to the 'ReadsPerGene.out.tab' files as output by STAR.
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- name: "--output"
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type: file
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direction: output
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default: "starLogs.txt"
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description: |
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Tab-delimited file describing for each barcode (as the rows), the metrics (as columns)
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gathered from the different input files.
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resources:
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- type: python_script
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path: script.py
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test_resources:
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- type: python_script
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path: test.py
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- path: test_data
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engines:
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- type: docker
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image: python:3.12-slim
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setup:
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- type: apt
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packages:
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- procps
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- type: python
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packages:
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- pandas
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test_setup:
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- type: python
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packages:
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- viashpy
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runners:
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- type: executable
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- type: nextflow |